Question: Scoring matrix of 3 sequence alignment
gravatar for mhasa006
4.5 years ago by
United States
mhasa00650 wrote:

I want to perform global sequence alignment on 3 DNA sequences. Now while making the scoring matrix for the dynamic programming, there are 7 possible cases. In case of 2 DNA sequences, the options are either a match or a insert or delete. But in 3 sequence alignment, there are all three match, two match and a gap and two gaps. 

Is the following observation of mine is right?

1. For exact match in three sequence I just add the matching score in the scoring matrix
2. For two match and a gap I added (matched scored + gap) (i.e. matched score = 2, gap = -2)
3. For two gaps I added (gap * 2) in the scoring matrix.

Is these observation correct?

ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by mhasa00650
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